BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR054602.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 10,094,079
number of mapped reads = 8,098,480 (80.23%)
number of supplementary alignments = 250 (0%)
number of secondary alignments = 0
number of mapped bases = 382,367,282 bp
number of sequenced bases = 382,284,477 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,707,921
duplication rate = 15.3%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.799
>>>>>>> ACTG content
number of A's = 116,757,386 bp (30.54%)
number of C's = 71,004,032 bp (18.57%)
number of T's = 117,514,884 bp (30.74%)
number of G's = 76,949,903 bp (20.13%)
number of N's = 58,272 bp (0.02%)
GC percentage = 38.7%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 1,910,358
number of insertions = 16,876
mapped reads with insertion percentage = 0.21%
number of deletions = 56,068
mapped reads with deletion percentage = 0.69%
homopolymer indels = 48.7%
>>>>>>> Coverage
mean coverageData = 0.1235X
std coverageData = 0.8663X
There is a 5.69% of reference with a coverageData >= 1X
There is a 2.32% of reference with a coverageData >= 2X
There is a 1.27% of reference with a coverageData >= 3X
There is a 0.79% of reference with a coverageData >= 4X
There is a 0.53% of reference with a coverageData >= 5X
There is a 0.37% of reference with a coverageData >= 6X
There is a 0.27% of reference with a coverageData >= 7X
There is a 0.2% of reference with a coverageData >= 8X
There is a 0.15% of reference with a coverageData >= 9X
There is a 0.12% of reference with a coverageData >= 10X
There is a 0.09% of reference with a coverageData >= 11X
There is a 0.08% of reference with a coverageData >= 12X
There is a 0.06% of reference with a coverageData >= 13X
There is a 0.05% of reference with a coverageData >= 14X
There is a 0.04% of reference with a coverageData >= 15X
There is a 0.04% of reference with a coverageData >= 16X
There is a 0.03% of reference with a coverageData >= 17X
There is a 0.03% of reference with a coverageData >= 18X
There is a 0.02% of reference with a coverageData >= 19X
There is a 0.02% of reference with a coverageData >= 20X
There is a 0.02% of reference with a coverageData >= 21X
There is a 0.01% of reference with a coverageData >= 22X
There is a 0.01% of reference with a coverageData >= 23X
There is a 0.01% of reference with a coverageData >= 24X
There is a 0.01% of reference with a coverageData >= 25X
There is a 0.01% of reference with a coverageData >= 26X
There is a 0.01% of reference with a coverageData >= 27X
There is a 0.01% of reference with a coverageData >= 28X
There is a 0.01% of reference with a coverageData >= 29X
There is a 0.01% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 34382109 0.13794191910960174 0.9618055993898581
chr2 243199373 32367181 0.1330890807847601 0.9296890941265623
chr3 198022430 28763857 0.14525555009096697 0.906023876378421
chr4 191154276 24924272 0.1303882524710041 0.8869978098855857
chr5 180915260 18944418 0.10471431763135956 0.7022374606836105
chr6 171115067 19279980 0.11267260293332322 0.804179736819228
chr7 159138663 24922133 0.1566063992883992 1.042577097760419
chr8 146364022 22879510 0.156319221673206 1.0060325476913674
chr9 141213431 18678710 0.1322728997357199 0.9351637084538914
chr10 135534747 16162250 0.1192480183697838 0.8343112143601958
chr11 135006516 16946195 0.12552131187505053 0.8835966079605159
chr12 133851895 13599766 0.10160308899623723 0.7003317964722804
chr13 115169878 12659244 0.10991801172178024 0.7418496716640973
chr14 107349540 8642519 0.0805082071148139 0.686194761205109
chr15 102531392 11945141 0.1165022805893438 0.7647794866052249
chr16 90354753 10036391 0.1110776208972648 0.820986976251609
chr17 81195210 6813637 0.08391673597494237 0.6083849508273451
chr18 78077248 14471623 0.1853500651047537 1.2093638868605798
chr19 59128983 6448102 0.10905146127745846 0.8315345232046378
chr20 63025520 6130894 0.09727637312631454 0.72672043113283
chr21 48129895 4859416 0.10096460837905423 0.8317471260761685
chr22 51304566 3945138 0.07689643062178911 0.5796612411040327
chrMT 16571 48274 2.9131615472813954 5.758012419349266
chrX 155270560 23569168 0.15179418429353253 0.9681269376581069
chrY 59373566 947354 0.015955821147747806 0.35231963416261064